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Summary Table of Jags Posterior Estimates

Source: R/post_summ.R
post_summ.Rd

post_summ() takes a list output from run_mod() to summary table for parameter, antigen/antibody, and stratification combination. Defaults will produce every combination of antigen/antibody, parameters, and stratifications, unless otherwise specified. Antigen/antibody combinations and stratifications will vary by analysis. The antibody dynamic curve includes the following parameters:

  • y0 = baseline antibody concentration

  • y1 = peak antibody concentration

  • t1 = time to peak

  • r = shape parameter

  • alpha = decay rate

Usage

post_summ(
  data,
  iso = unique(data$curve_params$Iso_type),
  param = unique(data$curve_params$Parameter_sub),
  strat = unique(data$curve_params$Stratification)
)

Arguments

data

A list outputted from run_mod().

iso

Specify character string to produce tables of only a specific antigen/antibody combination, entered with quotes. Default outputs all antigen/antibody combinations.

param

Specify character string to produce tables of only a specific parameter, entered with quotes. Options include:

  • alpha = posterior estimate of decay rate

  • r = posterior estimate of shape parameter

  • t1 = posterior estimate of time to peak

  • y0 = posterior estimate of baseline antibody concentration

  • y1 = posterior estimate of peak antibody concentration

strat

Specify character string to produce tables of specific stratification entered in quotes.

Value

A data.frame summarizing estimate mean, standard deviation (SD), median, and quantiles (2.5%, 25.0%, 50.0%, 75.0%, 97.5%).

Author

Sam Schildhauer

Examples

post_summ(data = serodynamics::nepal_sees_jags_post)
#> # A tibble: 20 × 11
#>    Iso_type Parameter_sub Stratification    Mean      SD  Median  `2.5%` `25.0%`
#>    <chr>    <chr>         <chr>            <dbl>   <dbl>   <dbl>   <dbl>   <dbl>
#>  1 HlyE_IgA alpha         paratyphi      2.30e-3 3.60e-3 1.16e-3 1.27e-4 5.30e-4
#>  2 HlyE_IgA alpha         typhi          3.60e-3 4.25e-3 2.04e-3 2.52e-4 1.02e-3
#>  3 HlyE_IgA shape         paratyphi      1.71e+0 3.14e-1 1.65e+0 1.27e+0 1.50e+0
#>  4 HlyE_IgA shape         typhi          1.68e+0 3.50e-1 1.60e+0 1.28e+0 1.43e+0
#>  5 HlyE_IgA t1            paratyphi      3.49e+0 1.47e+0 3.18e+0 1.49e+0 2.36e+0
#>  6 HlyE_IgA t1            typhi          7.85e+0 5.10e+0 6.87e+0 2.05e+0 4.57e+0
#>  7 HlyE_IgA y0            paratyphi      2.51e+0 9.51e-1 2.35e+0 1.04e+0 1.83e+0
#>  8 HlyE_IgA y0            typhi          2.98e+0 2.73e+0 2.44e+0 6.94e-1 1.75e+0
#>  9 HlyE_IgA y1            paratyphi      1.11e+3 8.68e+3 1.54e+2 7.89e+0 5.14e+1
#> 10 HlyE_IgA y1            typhi          9.96e+2 3.51e+3 2.05e+2 6.74e+0 6.89e+1
#> 11 HlyE_IgG alpha         paratyphi      2.55e-3 2.06e-3 1.99e-3 4.23e-4 1.18e-3
#> 12 HlyE_IgG alpha         typhi          2.05e-3 1.99e-3 1.47e-3 2.29e-4 8.36e-4
#> 13 HlyE_IgG shape         paratyphi      1.31e+0 1.24e-1 1.30e+0 1.12e+0 1.21e+0
#> 14 HlyE_IgG shape         typhi          1.47e+0 4.06e-1 1.37e+0 1.07e+0 1.22e+0
#> 15 HlyE_IgG t1            paratyphi      4.69e+0 1.88e+0 4.31e+0 1.99e+0 3.43e+0
#> 16 HlyE_IgG t1            typhi          7.89e+0 6.30e+0 6.34e+0 1.71e+0 3.88e+0
#> 17 HlyE_IgG y0            paratyphi      2.02e+0 8.72e-1 1.85e+0 1.01e+0 1.50e+0
#> 18 HlyE_IgG y0            typhi          2.05e+0 1.67e+0 1.71e+0 3.40e-1 1.08e+0
#> 19 HlyE_IgG y1            paratyphi      4.36e+2 7.47e+2 1.91e+2 1.42e+1 8.00e+1
#> 20 HlyE_IgG y1            typhi          6.16e+2 2.12e+3 2.36e+2 1.92e+1 1.03e+2
#> # ℹ 3 more variables: `50.0%` <dbl>, `75.0%` <dbl>, `97.5%` <dbl>